If you run an e-commerce business, you know there’s a lot coming your way. Purchasing products, answering customer questions, running ads, processing returns… And then there’s the bookkeeping. Unfortunately, that often gets underestimated – even by some bookkeepers.
E-commerce has its own unique dynamics, and a standard bookkeeping approach often doesn’t work well. In this article, we’ll share the most common mistakes made in webshop accounting – and more importantly: how to avoid them.
1. Recording Shopify or Bol.com payouts as ‘revenue’
This one often goes wrong. You receive a payout from Bol.com or Shopify Payments, and it’s directly recorded as revenue. Sounds logical, right? But that amount is usually already net of fees, returns, and discounts. So what you’re actually booking is your net profit, not your revenue.
What you should do instead:
Use tools or exports that show the full breakdown: gross revenue, returns, platform fees, transaction fees… That’s how you’ll really gain insight into your numbers.
2. Incorrect VAT application on international sales
Selling within Europe? Then you’re dealing with different VAT rates, thresholds, and – if set up properly – the OSS system. Many bookkeepers stick to Dutch VAT or forget to differentiate between countries at all.
Result:
Incorrect filings (hello fines) or even double VAT payments. Totally avoidable and unnecessary.
Tip:
Activate OSS with the Dutch tax authorities if you sell to multiple EU countries. And make sure your bookkeeper clearly sees where your customers are based. Looking for a good bookkeeper with e-commerce expertise? Schedule a free call [here].
3. Lumping shipping costs together
It’s common to see shipping costs get lumped together somewhere in the expenses, without distinguishing between what you pay to PostNL or DHL, and what you charge the customer.
Why that’s not helpful:
You won’t know if you’re making a profit, breaking even, or losing money on shipping.
What to do instead:
Record shipping separately: one entry for shipping income from customers, and another for the actual costs from your carrier(s).
4. Recording inventory as a cost instead of an asset
If you purchase €10,000 worth of inventory, that’s not an immediate expense. Yet it often gets recorded that way. But inventory is an asset and belongs on your balance sheet, not in your profit and loss statement.
Result:
Your profit looks lower than it really is. And you have no idea how much inventory value is still on your shelves.
Better approach?
Maintain proper inventory records (even a simple Excel sheet is a good start). Ideally, link your webshop to an accounting tool that includes inventory tracking.
5. Dumping all costs into one category
Meta Ads, fulfillment fees, Bol or Amazon platform fees… They often end up in one big pile of “sales costs.”
Downside:
You can’t see which channel is most profitable – or which one is draining money.
Tip:
Create separate expense accounts or labels per channel. That way, you can make strategic decisions based on what’s actually working.
6. Ignoring exchange rates on international sales
Selling in dollars or pounds through Amazon or PayPal? Then you’re dealing with currency exchange rates. Many bookkeepers just record the incoming amount and ignore the exchange rate differences.
Result:
Small differences add up, and your numbers no longer align accurately.
How to fix it:
Record exchange rate gains/losses separately. Most bookkeeping tools have a specific general ledger account for that.
7. Doing everything manually
Manually transferring data from Shopify into your bookkeeping system is just asking for mistakes – you’ll often miss a number, and it’s super time-consuming.
What’s smarter:
Use integrations! Tools like Exact Online, Moneybird, or e-Boekhouden can connect directly to your webshop or payment provider.
Automation = fewer errors and more peace of mind.
Want to know how we can help you automate? Schedule a call with one of our experts below.
